The Second Strain
by Crystal di Angelo
Summary: The Flare works in many diverse ways. Group A's non-Immune, Newt is one of the unfortunate ones. Which strain would lead to a better death, the First or the Second?
1. Chapter 1

**Weird idea time: What if the Flare worked in more diverse ways?**

 **In which I sadistically torture Newt (again. Refer to Prototype, my other story).**

 **Dylan O'Brien was just so adorable when presenting the Death Cure set! And the few glimpses of Thomas Brodie-Sangster had managed to snap me out of the stupor I had gotten into over an actor in a Singaporean drama (he stopped acting after 2012...ish...and I'm bemoaning the lack of media). Hence the reawakened Maze Runner fervor.**

 **I'm going to leave you in the dark about this first, except that this is totally AU. It deviates almost completely from the books and movies after the second one. It's not going to be long, five chapters at the most. Then again, I'm rubbish at estimations. I don't even have a clear plot line for this yet.**

 **Enjoy!**

* * *

 _It had shown itself in the Scorch, brief glimpses and brushes, but they didn't truly understand what it meant._

* * *

"Rise and shine, shanks! We have to get moving fast if we're going to reach the village before night!"

The Gladers rose reluctantly, brushing sand from their clothes. Thomas groaned and resisted the urge to flip over on his side to avoid the glare of the Sun shining down on them. Beside him, Newt sat up, seemingly unbothered by the harsh sunlight.

"It's still dark out, Min."

"Huh?" Thomas turned sharply to face his friend, tiredly rubbing at his eyes. Minho let out a snort of disbelief.

"Now's not the time to shucking kid me for a few more seconds of sleep, Newt."

Newt blinked a few more times. "Oh. The sun's glare must have blinded me. Shucking brilliant."

They continued on their journey, the little episode forgotten as they struggled to survive.

Until more started to crop up.

Minho barely managed to yank Newt out of the way as the passage crumbled. He would have reached for Thomas too, but Newt was responding too slowly, and it was the best he could do to make sure that none of the falling chunks of rocks hit them.

He coughed, dust shifting around him, and the dust settled enough for him to see Newt staring open-mouthed at the damage. The blocked tunnel. He was about to open his mouth when he heard Newt mutter quietly, to himself.

"How the bloody hell did I not hear _that_?"

And more.

"This tastes like klunk!" Newt complained, wrinkling his nose after getting a bite of the rations.

Frypan stared curiously at him. While it wasn't gourmet food, it was edible and decent. He wondered if his cooking was that good, to spoil Newt to this extent.

"Shut it, shank. It's something, so eat it and shut your hole." Minho sat down beside Newt, stretching his legs after a long day of running. He had been irritable lately, even with Newt. _Especially_ with Newt.

Newt said nothing, just quietly finished the rest of the energy bar.

Frypan saw genuine confusion flicker in his Second in Command's eyes for a moment, but it was gone in an instant.

And the one that made everyone notice that something was genuinely wrong.

"Run for the Berg!" Thomas screamed over the sound of gnashing teeth and screams. "Quick! They didn't plan to wait for us!"

Struggling with their respective opponents, the Gladers, Glenners, Jorge and Brenda slowly made their way in the general direction of the Berg, more and more bodies thudding to the ground.

"Aim for the bulbs!"

Thomas quickly ran to help out the others as soon as he discovered the Achlles' Heel of whatever these things were, doing us best to ignore the blood soaking into the dry desert ground. Thunder crackled above them ominously.

In the instant lightning flashed, he heard a surprised yelp to his left, and spun to find Minho tackling a not-Griever, with two final bulbs dangling tantalizingly on its body down as Newt stared at his makeshift weapon, a staff on the ground, concentrating so hard that Thomas would have assumed that he was trying to move it by telekinesis.

Then the moment was over, and Newt moved, quick and deft, snatching the staff up from the ground, and with two well aimed jabs, he burst the remaining two bulbs. An unreadable expression on his face, he offered Minho a hand up.

Minho took it, and was about to say something when the Berg started moving, gaining speed.

"SHUCK!" Newt yelped, and the three of them sprinted after their salvation, barely making it, tumbling into the Berg painfully just as it took off.

"Now, shank." Minho said, after taking stock of their environment, rounding on Newt. "Tell me what the shuck happened out there."

He wished he hadn't asked.

"I don't know." Newt whispered.

In that moment, he looked very much like a frightened child.

* * *

Thomas couldn't stop worrying about Newt, and it drove him up the walls when he was being held in the White Room. When he saw everyone together at the end of the Third Trial, he wanted to pounce on Newt and ask him whether those episodes had still been happening, but Newt looked so happy and relaxed, teasing Minho about the new haircut he'd wrangled from a guard, that he couldn't bring himself to spoil it.

The Rat Man cleared his throat, and the room fell silent.

"Well, subjects-"

"Stop calling us that." Harriet, sounding annoyed. "Gladers and Glenners will do."

"Ladies and gentlemen." Jansen opted for a compromise, though sniggers were heard around the rooms to being addressed like this. "Congratulations on completing the Trials. You are now officially free from them."

"Oh yeah? What about our memories?" Frypan called out.

"I'm getting to that. You will all be of greater use to our research for a Cure to the Flare with your memories intact, so we are going to remove the Swipe shortly after this. It is a painless and swift procedure, and the only side effects you will experience is minor disorientation."

With those words, the room was thrown into an instant uproar.

"-trust them-"

"-our memories!"

"I want to-"

"Wait, you don't have the Cure yet?"

The room was silenced instantly.

"We hope to have one very soon." Janson said, his smile unwavering. "You are all Immune, which is why you have been chosen to take part in the Trials. We want to know what adaptive structure you might have in your Killzone to combat the Flare, and we hope to duplicate it."

A collective sigh of relief was heard.

"However, a few of you have been placed in the Trials as Controls, to compare your brain patterns. I'll like to get this over as soon as possible. The Controls are advised to remain in the facility as they will be high up in the priority list for receiving the Cure."

The room tensed again, everyone waiting for the hammer to fall.

"Group A, Subject A5, the Glue, Isaac Newton. Group B, Subject B8, the Provider, Margaret Thatcher. Now, will those who wish to have the Swipe removed follow me?"

Janson breezed through the announcement, as though happy to have yet another task ticked off the list.

"Newt..."

"I'm a Crank." Newt said, voice hollow. "I'm a Crank, Min."

Thomas sat quietly by the side, absorbing the new information, watching Margaret take quick, uneven strides out of the room after Janson. The rest soon followed.

Minho pulled the smaller boy into a gruff hug, a rare of affection. "It's going to be alright. Those shuckfaces will find a Cure, and you're going to get better."

Newt started to cry into Minho's shoulder. "It's not that, Minho, it's not just that. The Flare doesn't explain what's been going wrong with me. The Flare is supposed to make me mad, and I know how to deal with that, I've been thinking about it the whole way here, but there's something else, and I don't know what's happening in my bloody head. I'm _scared_ , Min."

"What's been going on?" Thomas asked, trying to make his voice as soothing as possible.

Newt lifted red, unfocused eyes to his. "I can't see, Tommy."

* * *

 _"Fascinating. This mutated strain of the Flare hasn't been seen in nearly a decade."_

 _"Why?" The trainee asked._

 _"Because they were wiped out by those who contracted the First Strain. Those who contract this usually can't survive long. Not long enough to pass it on. But somehow, our Control seems to have contracted it from either the Scorch, or his physiology was designed to change the First Strain into the Second Strain. The latter is more probable, since the Second Strain died out a long time ago. Do you know what this means?"_

 _"If his body can mutate the Flare, we can use a similar theory to mutate the Flare into something harmless?"_

 _Janson smiled. "And this is why you are Ava Paige's protégée."_


	2. Chapter 2

_One contracts the Flare through the air._

* * *

Thomas walked into the room filled with white, sterile machines, strides even, purpose clear.

"I want the Swipe removed."

"Excellent choice." Janson beamed at him, almost as if he was commending a son proudly.

Thomas resisted the urge to turn tail and run, to vomit.

For he had a very strong reason for his choice.

The blond currently being led into the same room by Minho, a guiding hand on his shoulder.

The needle pricked his skin.

* * *

"You don't have to do this, Tommy."

"I have to. I won't forgive myself if I didn't even try. They said I was one of the major forces here. If I can figure out what's going on, how the Flare is messing with your brain..."

"But what if it isn't the Flare?"

* * *

Thomas woke to sounds of steady beeping and soft mumbling.

"His patterns are active again. Mr. Edison. Welcome to WICKED."

Thomas realized that it was no use feigning sleep and opened his eyes.

"Johnson." He greeted the nurse curtly, the name slipping naturally out of his mouth. "I believe I had left three incomplete folders of research to you before the Maze."

Alicia Johnson nodded, snapping into business mode. "Yes, Mr. Edison. Two have been completed by the teams you assigned, but since you said that the third one was of minor importance, we reassigned the team to the Maze Trials. Would you like to see the completed files?"

Just his luck.

"Bring me the incomplete one. The Second Strain."

* * *

Minho had some serious doubts about Thomas giving himself into the hands of WICKED again, and Newt had raised several valid arguments, but Thomas insisted that the benefits outweighed the risks.

In the end, they compromised that Minho would not remove the Swipe, and thus having one person at hand to knock some sense into Thomas in case WICKED did try something.

Janson had happily allowed that, satisfied that their Top Candidate had decided to cooperate. He had thrown a weird look at Newt though, an odd smile on his lips. Minho would have punched him if not for the fact that he would be operating the machine that would drill a hole into Thomas' skull in five minutes.

Newt still didn't like the idea though.

"Seriously, it's not that bad. I'm starting to see colors again now." He grumbled, though nearly tripped over the doorframe as Minho led him into their assigned room.

"Whatever you say, slinthead." Minho snorted. He automatically catalogued his surroundings as he led Newt to the bed, giving him the lower bunk.

Two bunks. Two desks, with drawers. No windows. Vents, through which cool air was being pumped. A second door, which he presumed to be the washroom. The door they entered through had a flap in it, presumably for meals. Minho didn't like what that insinuated, that this room was designed for confinement. The pristine white of everything in there irked him. He also noticed that there was no third bed.

Thomas would be separated from them.

Newt cautiously felt around the bed, then threw himself on it after getting a general idea of its width. The mattress was thin and hard, but it was a bed, and Newt wasn't going to complain.

"Y'know...when did you realize that you couldn't see?" Minho finally asked, as he absentmindedly rifled through the drawers of the desk, finding two sets of pristine white clothes.

"It started during the Third Trial." Newt said quietly, folding his hands together. "One second they were showing me something, the next I just blacked out. I thought I passed out at first, but then I was still standing. I panicked. Tried to destroy their screens. They sedated me and I woke up able to see."

"And today?" Minho pressed, curious about what Newt's trial had entailed, but at the same time realizing that he would have to give up information about his own trial as well, which he didn't want to.

"The second Rat Man said I had the Flare...everything went black again." Newt closed his eyes and reopened them, finally seeing Minho's face swim into blurry focus. "I can see now. Are those clean clothes?"

Minho tossed a set to Newt, frowning as he found two name tags at the bottom of the drawers.

"I call dibs on the shower!" Newt snatched his clothes out of the air and dashed to the washroom, eager to be rid of the grime clinging to him.

"By all means, you prissy princess!" Minho called out as Newt closed the bathroom door. "And don't lock the door! If you suddenly go blind again I don't want to have to break down that door to save your shuck ass when you knock yourself out on something or the other!"

" _You_ are the princess! Don't pretend you don't spend hours styling your hair every morning!"

Minho sighed and shook his head as the sounds of water running started. He looked at the tag and felt his heart sink.

 _Isaac Newton_

 _Subject A5_

 _The Glue_

 _Engineering Divisions Assistant Director_

He dropped Newt's tag and frantically went for his own set, shaking the clothes until the tag fell out.

 _Minho Lee_

 _Subject A7_

 _The Leader_

 _Physical Division Assistant Director_

 _No._

He flipped both tags over.

On Newt's was a handwriting he'd know anywhere. Newt had mostly been in charge of sending down notes for the Creators, since he had the most legible handwriting out of the all of them, was less prone to making mistakes (their writing materials were limited!) and had a way of wording their requests to be really persuasive.

 _Notes: MUST IMPROVE MAZE DOORS DESIGN! Too much energy consumption!_

 _Lunch is at 1.00 at Block A starting June._

 _BLOCK A! Stop going to B!_

 _Creches for ivy growth need to be added._

And his own handwriting.

 **Stop pretending you're listening to Paige's nonsense.**

Minho looked at his own tag, unable to process this new development.

 **Important test at 12.00 tomorrow. Must show up.**

 **Make up test at 8.00 next Monday. MUST SHOW UP.**

 **Tell Newt to remind me to show up for make upx2 test at 14.00 on Wednesday**

 _Oh, shut up._

Minho stood there for a moment before chucking both tags into the drawers and slamming them shut. He was trembling, whether from rage or fear he did not know.

They had worked for WICKED. Willingly.

Newt had designed the very walls that later became a medium for his suicide attempt.

He had done...something. Physical. Probably kept checks on the subjects' physical condition.

Minho swallowed down the rising bile in his throat. Subjects. In his mind, he had automatically addressed everyone as subjects.

He wasn't sure how long he had stood there, mind whirring through all the implications and possibilities, but when the sound of running water ceased, he hastily sprang into action, tucking the tags into the folds of his own clothes as Newt opened the door partially, frowning.

"Min, pass me that clean set of clothes, will you?"

"Trust you to forget your shucking clothes when you get in the shower." Minho smirked, turning to pass the set of clothes to Newt.

Newt frowned at him. "What's wrong? You look like you've seen a bleedin' ghost."

* * *

"The Subjects are responding well." Thomas noted. He did his best to push away the niggling feeling in the back of his mind that he should not be continuing his work for WICKED, that he had felt what it was like to be a lab rat and wouldn't wish that fate on anyone else, let alone his best friends.

But he had to save Newt.

Watching Minho trying to bluff his way past the blond with narrowed eyes, Thomas could almost believe that he was doing the right thing. For his friends. For the world.

"That was quite the innovative idea, Thomas." Ava Paige murmured from her position beside him, eyes fixed on the screen as well. Scientists were by the side printing out the wavy patterns of the duo as they spoke. On another screen, Frypan and Danny were turning over their respective tags, a mixture of awe and sadness on their faces.

Teresa was at the large holo-table in the middle of the room, dark hair spilling down her face as she worked feverishly, trying to incorporate the new patterns into their current blueprint. Truth to be told, the blueprint seemed like a colossal waste of effort and time, but it was their only shot. They were to find constants in the patterns of the Immunes, compare it with the Controls who were exposed to the same situation and slowly, create a basic idea of how the Immune brain works. Then they would need to train surgeons to make the necessary modifications in the Cranks.

If they trained ten surgeons in a year, and each surgeon could save only one person a day, due to the complex nature of neurosurgery, with the current twenty million population of surviving Cranks, and non-Immunes, it would take years to save them all. Time and resources that they would be hard pressed to provide.

Thomas yanked himself away from the depressing numbers. For now, he would focus on things one at a time.

Save them one at a time.

He hoped that Minho, Newt and the others would be able to forgive him for this.

They had to.

Because they hadn't needed to fake those tags.

* * *

They both knew that this wasn't the end of the matter.

But Minho was tired, and Newt's eyesight was starting to deteriorate again, so eventually Newt pretended to buy Minho's act and they turned in for the night.

Minho knew better than to think that the keen blond would just let the matter go like that. There was a reason Alby had chosen him as the second in command, unlike what some had assumed, that Newt had gotten the job simply because he could do nothing else with that shucked up leg of his.

Newt was a quick thinker, flexible and sharp. Alby had the advantage of being intimidating, but Newt was scarily attuned to everyone's emotions, which made him dangerous, especially if he was playing the nice guy with a limp whom no one would be wary of.

Having been in the Maze with Newt since Day One, surviving, fighting, devising a system and making hard decisions together, Minho knew enough to slip the tags into his pillowcase when Newt wasn't watching.

The next day, Minho woke early, due to his natural body clock having been attuned to the days of working as a Runner, rising at the crack of dawn before spending yet another day in the Maze. Newt was still asleep, curled in a fetal position with blankets bunched around him. No doubt he was catching up on much needed sleep, with all the stress in the Scorch and the Third Trial, no one had really slept well.

Perfect.

Minho climbed onto the upper bunk again, retrieving the tags from his pillowcase and looking them over again. It was safe to assume that they were expected to wear them to whatever event WICKED had planned for them today, having been placed with their clothes.

Except that Minho didn't want to put it on. And he had no intention of letting Newt see them either.

They had worked for WICKED.

Minho could come up with a thousand excuses, that they were forced to, that the tags were faked. But it still doesn't change the fact that the seed of doubt had been planted.

Newt had bottled up enough already, wearing smiles and giving hope until the day he plummeted from the wall. And it broke Minho's heart that, even though now he had learned to look for the signs, Newt's habit of keeping things in had not changed.

Even with his own slightly better attitude of taking revelations in stride and not dwelling upon them, Minho could still feel the self loathing rise as he looked at the scribbles on the tags. So casual and carefree. Like they weren't discussing plans to trap and kill dozens of kids in a giant Maze.

Making a decision, Minho quickly scrambled down the ladder and went into the bathroom. He tore the paper to pieces, ignoring the fact that they might be the last clue to their life before that they had. He ignored the fact that Newt might have wanted to know, to see this.

He flushed them down the toilet bowl, then relieved himself and flushed once more to make sure it was gone. Satisfied, he exited the washroom, briefly glanced at Newt once more to make sure that he had heard or seen nothing of it, and clambered back onto his bed to continue sleeping.

Below him, Newt opened his eyes.


End file.
